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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Data & Tools
Home › Data & Tools › Data Management Practices and Resources

Data Management Practices and Resources

Read JGI’s Data Policy

Read the DOE Office of Science Statement on Digital Data Management

Current Data Management Practices

Raw sequence data—Raw data produced by the DOE JGI’s sequencing platforms are base-called in real time and primary (image) data are discarded shortly after base-calling is complete.  Sequence data are stored as FASTQ files containing the linear sequence and associated quality scores.   All primary sequence data receive automated quality control screening to assess sequence quality and quantity, identify major contamination, and confirm that the data generated correspond to the expected organism/environment being sequenced.  For most sequencing projects, raw sequence data is made available to registered users through the genome-specific portal web page and are submitted to NCBI’s Sequence Read Archive (SRA) as soon as the embargo defined by the JGI Data Policy has ended.

Processed sequence data—For most user projects, the DOE JGI conducts standard post-sequencing analyses that vary by project type (see Product Offerings).  These analyses and associated metadata are available for download from project-specific data portals to the DOE JGI data users after the embargo has ended. User-selected subsets of public data can also be downloaded from the DOE JGI’s comparative analysis platforms as described in Data Resources below.  Beginning in fall 2013 users wishing to download data from the DOE JGI portals will be required to register with the DOE JGI.

Project metadata—Every user project has associated metadata that are important for interpretation of the data produced.  These include, for example, authors of the data, PI contact information, detailed sample information and details of analyses performed.  These data will be served with processed data from the DOE JGI’s data portals whenever possible, however metadata for older legacy projects may be limited.

Data archive and back-up—All data available for download by users is automatically archived onto a high-speed tape system located at the National Energy Research Scientific Computing facility (NERSC).  A second redundant copy of these data is also stored on high-speed tape (but not on the same cassette!).  Typical retrieval times range from minutes to hours depending primarily on file size.

Data Management Resources

The DOE JGI provides some resources to users to facilitate analysis of genomic data produced outside of the DOE JGI or to allow post-hoc analysis of DOE JGI data.  Because these resources are supported through public funds it is expected that such analyses and externally created data managed with these resources will be made public at the time of publication.  The user bears sole responsibility for providing and maintaining public access to these data and analyses.

Phytozome —The DOE JGI’s comparative genomics platform for plants allows user-driven filtering of plant genome data by characteristics of interest that are then downloadable by individual users.  Phytozome does not currently keep these analyses nor support their display for other users.  Phytozome supports the display of user-provided genome tracks that are compatible with GBrowse, but does not generally display these tracks for other users.  By mutual agreement between JGI and the data providers, Phytozome may display non-DOE JGI genomes for comparative purposes or additional genome-anchored data for DOE JGI genomes. The DOE JGI will make these data public and downloadable following the embargo, but responsibility for depositing these data in public repositories resides with the data provider.

MycoCosm and PhycoCosm —The DOE JGI’s comparative genomics platforms for fungi and algae support user-driven filtering of comparative genomics data by characteristics of interest that are downloadable by individual users.  These platforms support manual curation of genome annotations by registered users who have received specific training.  These annotations are in turn served to the user community.  MycoCosm and PhycoCosm may display genomes and annotations created elsewhere by mutual agreement between JGI and the owners of the external genome data. JGI will make these data public and downloadable following the embargo, but responsibility for depositing these data in public repositories resides with the data provider.

Integrated Microbial Genomes platform (IMG)—IMG supports user-driven filtering of comparative genomics data by characteristics of interest and maintains results for users. Results of comparative analyses are downloadable and may be shared with other users within the IMG system.  Responsibility for providing public access to these data at the time of publication is the sole responsibility of the user.  Isolate genomes, single cell genomes and metagenome datasets produced elsewhere may be uploaded for annotation and analysis within IMG. Data must be made public at the time of publication and this responsibility lies with the user.

Genomes OnLine Database (GOLD)—GOLD is an online database of worldwide genome projects and associated metadata that is maintained for the public by the DOE JGI. The data are filterable and downloadable.  Users may register their genome projects in GOLD, but must agree to make the registration and associated metadata publicly available at the time of publication.  Registration of non-DOE JGI genome projects with NCBI or other public registries is the sole responsibility of the user.

DOE JGI’s Policy on Microbial Genbank Submissions

Microbial genome sequencing projects become eligible for preparation for submission to Genbank when they become public in the Integrated Microbial Genomes system following the embargo. This includes sequences from both cultured organisms and single cells sequenced at DOE JGI only*.

All eligible projects are prepared as WGS submissions. Although JGI has been submitting annotated genomes to Genbank in the past, moving forward we will only support WGS submissions and will serve annotations through IMG.

For questions, please contact Galina Ovchinnikova.

* Please note that genomes submitted by external users for annotation and comparative analysis in IMG are not automatically submitted to Genbank.

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